Rsta.2012.0304

rsta.royalsocietypublishing.org
Review
Cite this article: Mali KS, De Feyter S. 2013
Principles of molecular assemblies leading to
molecular nanostructures. Phil Trans R Soc A
371: 20120304.
http://dx.doi.org/10.1098/rsta.2012.0304
One contribution of 17 to a Theme Issue
‘Molecular nanostructure and
nanotechnology’.
Subject Areas:
supramolecular chemistry
Keywords:
self-assembly, molecular nanostructures,
non-covalent interactions, monolayers,
scanning tunnelling microscopy
Author for correspondence:
Steven De Feyter
e-mail: steven.defeyter@chem.kuleuven.be
Principles of molecular
assemblies leading to
molecular nanostructures
Kunal S. Mali and Steven De Feyter
Division of Molecular Imaging and Photonics, Department of
Chemistry, KU Leuven-University of Leuven, Celestijnenlaan, 200 F,
3001 Leuven, Belgium
Self-assembled physisorbed monolayers consist of
regular two-dimensional arrays of molecules. Two-
dimensional self-assembly of organic and metal–
organic building blocks is a widely used strategy
for nanoscale functionalization of surfaces. These
supramolecular nanostructures are typically sustained
by weak non-covalent forces such as van der
Waals, electrostatic, metal–ligand, dipole–dipole and
hydrogen bonding interactions. A wide variety of
structurally very diverse monolayers have been
fabricated under ambient conditions at the liquid–
solid and air–solid interface or under ultra-high-
vacuum (UHV) conditions at the UHV–solid interface.
The outcome of the molecular self-assembly process
depends on a variety of factors such as the nature of
functional groups present on assembling molecules,
the type of solvent, the temperature at which
the molecules assemble and the concentration of
the building blocks. The objective of this review
is to provide a brief account of the progress in
understanding various parameters affecting two-
dimensional molecular self-assembly through
illustration of some key examples from contemporary
literature.
1. Introduction
Molecular synthesis, which constitutes a sizeable part
of chemistry, is usually considered in the context of
breaking and making of covalent bonds between atoms
and molecules. On the other hand, relatively weaker
non-covalent interactions, such as van der Waals forces,
hydrogen bonds, π–π stacking, electrostatic and dipole–
dipole interactions, can collectively be equally strong
and play an important role in determining various
material properties. These interactions have been used
2013 The Author(s) Published by the Royal Society. All rights reserved.

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rsta.royalsocietypublishing.orgPhilTransRSocA371:20120304
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in Nature for building complex supramolecular architectures via the process of biorecognition
and biomolecular organization. Taking inspiration from Mother Nature, researchers have already
begun to fabricate complex self-assembled architectures in which individual components interact
via non-covalent forces. Described as the ‘chemistry beyond the molecules’ [1,2], this field
has already permeated through most of chemistry and extended to the diverse array of other
disciplines, including biology, physics, materials science and engineering.
Molecular self-assembly has been recognized as a very promising strategy for controlled
bottom-up fabrication of functional nanostructures with tailor-made properties. The process
of molecular self-assembly in solution has been extensively studied over the years and has
contributed significantly to the general understanding of supramolecular interactions [3]. In
contrast to their solution-phase assembly, assembling molecules on solid surfaces imparts
a high degree of coherence in their alignment and packing, leading to well-defined two-
dimensional nanostructures. Such surface-confined molecular layers can be used for nanoscale
functionalization of surfaces with potential applications in diverse domains of science and
technology. However, despite a myriad of investigations carried out since the seminal work
of Foster & Frommer [4] and Rabe & Buchholz [5,6], most of the early findings on molecular
self-assembly on surfaces were serendipitous. This is because the intermolecular interactions
involved in the process are usually numerous, subtle, cooperative, multifaceted and have very
little directionality (with the exception of hydrogen bonding). To explore the real potential of
this approach, it is imperative to develop a clearer understanding of the various parameters
that govern self-assembled network formation on surfaces. The present review discusses the
principles of two-dimensional molecular self-assembly leading to the formation of well-defined
arrays of molecules on surfaces as observed by scanning tunnelling microscopy (STM) [7]. The
immensely popular class of chemisorbed self-assembled monolayers [8] (SAMs; for example,
alkyl thiols on gold) is not discussed.
STM has been the method of choice for visualization as well as manipulation of these
molecular layers in detail [9–14]. It allows imaging of these thin molecular layers adsorbed on
atomically flat conductive substrates such as highly oriented pyrolytic graphite (HOPG) and
Au(111) with submolecular resolution. A wide variety of structurally very diverse monolayers
have been reported ranging from simple lamellar patterns to hierarchically structured complex
multi-component systems. A vast majority of these studies deal with the structural aspects of
monolayers and revolve around construction of two-dimensional supramolecular networks in
a pre-programmed fashion. Just as in three dimensions, crystal engineering in two dimensions
deals with elements of the well-known repertoire of non-covalent interactions that define
supramolecular chemistry. The term ‘two-dimensional crystal engineering’ [15–22] has become
increasingly recognized in recent years. One of the most extensively investigated facets is the
structural polymorphism in these so-called two-dimensional crystals, wherein two different
crystalline packings can be obtained upon deposition of a single building block. A number of
experimental parameters have already been identified that control the appearance of a certain
type of polymorph over another. A non-comprehensive list of these parameters includes the
type of solvent [23–29], the concentration of molecules [30–35], the type of substrate [36–41], the
temperature at which the self-assembly takes place [42–45] and the thermal history of the sample
[46]. How these parameters affect the self-assembly of organic building blocks is the subject of
this review, with a special focus on the liquid–solid interface.
2. Basics of molecular self-assembly on surfaces
The complexity of surface-confined molecular assembly process stems from the inherent intricacy
of the adsorption process itself. The basic mechanism of all bottom-up fabrication strategies is
that they essentially represent one or the other type of growth phenomenon. Typically, molecules
are deposited onto a surface and, through a variety of processes involving intermolecular and
interfacial interactions, nanometre-scale structures evolve. This phenomenon is a non-equilibrium
process by default and is governed by a competition between kinetic and thermodynamic factors.

3
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These factors differ significantly when self-assembled network formation under UHV conditions
is considered against that at the liquid–solid interface. Adsorption at the liquid–solid interface is
complicated by the presence of the supernatant liquid (typically an organic solvent) phase as
well as the free exchange between the molecules adsorbed on the surface with those present
in the liquid (solution) phase. Thus, apart from the intermolecular and molecule–substrate
interactions, molecule–solvent and solvent–substrate interactions play a crucial role at the liquid–
solid interface. In the absence of solvent, the complexity of the adsorption process is significantly
reduced when molecules assemble at the UHV–solid interface [47,48].
Self-assembly on surfaces is primarily governed by a delicate balance between intermolecular
and interfacial interactions. At room temperature, most low molecular weight organic
compounds are too mobile and adsorption is favoured only when their adsorption energy (Eads) is
higher than their kinetic energy (Ekin). Interactions between adsorbed molecules are also crucial
for the evolution of ordered networks. Intermolecular interactions should be strong enough to
trap the molecules in a two-dimensional matrix, yet sufficiently reversible so that they allow
for repair of defects. If the intermolecular interactions are too strong then the molecules ‘stick’
to each other irreversibly, preventing the formation of an ordered equilibrium structure. This
condition necessitates that the intermolecular interaction energy (Eint) is only slightly higher
than Ekin. In addition to the aforementioned energy considerations, the surface diffusion barriers
(Edif) of the molecules on a given surface are also very crucial. The optimal relationship between
various energies relevant to the surface self-assembly process thus can be given as: Eb > Einter ≥
Ekin > Edif. Whether the adsorption of molecules leads to the formation of a kinetically trapped
metastable or thermodynamically stable equilibrium structure is governed by how quickly the
molecules adsorb and how fast they move on the surface. If the rate of adsorption is faster
than the surface diffusion rate, then molecules are not able to reach the equilibrium structure
and are trapped in a diffusion-limited state. On the other hand, if the adsorption rate is slower
or comparable to that of surface diffusion, then such a process leads to a thermodynamically
favoured equilibrium structure [47,48].
The liquid–solid interface provides an experimentally simple alternative to self-assembly
at the UHV–solid interface. However, as mentioned before, self-assembly at the liquid–solid
interface is complicated by the presence of a third component, namely the solvent, which acts
as a reservoir of molecules. The choice of solvent affects the mobility of molecules, especially
the adsorption–desorption dynamics via the solvation energy and possibly also via the solvent
viscosity. Once a drop of solution is applied onto a substrate, the dissolved species can diffuse
towards the substrate, adsorb, diffuse laterally and desorb. The monolayer is thus in a dynamic
equilibrium with the dissolved molecules in solution and constant adsorption–desorption is
likely to prevail on time scales relevant for typical STM experiments [49]. This spontaneous
dynamics is considered to be one of the main advantages of molecular self-assembly at the
liquid–solid interface, because it favours the repair of defects. Thus, it was generally believed
that self-assembly at the liquid–solid interface warrants the optimum conditions to achieve
equilibrium and hence leads to formation of thermodynamically stable structures. However, there
is increasing evidence that some of the two-dimensional molecular networks formed at the liquid–
solid interface are in fact kinetically trapped structures and may not represent the minimum
energy equilibrated state [46].
3. Role of the substrate and the medium
Despite their relatively weak nature, the molecule–substrate interactions have a strong bearing
on the adsorption of molecules [36–41]. Detailed experimental and theoretical studies have
revealed that the tendency of molecules in a two-dimensional monolayer to comply with the
registry of the substrate lattice can result in significant changes in intermolecular interactions
when compared with their self-assembly in three-dimensional crystals [36]. A wide range
of atomically flat metal and semiconductor surfaces can be used under UHV conditions;
however, many of them are not stable under ambient conditions. Therefore, HOPG has been

4
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a substrate of choice, although other substrates such as Au(111), MoS2 and MoSe2 are also
used under ambient conditions. The popularity of HOPG for such studies stems from the
fact that it is inert, easy to clean and very stable under ambient conditions. Apart from
these advantages, graphite also has a specific epitaxial interaction with alkyl chains which
arises owing to the similarity between the zig-zag alternation of methylene groups and the
[100] direction of the graphite lattice. Moreover, alkyl chains are stabilized by interchain
interactions (interdigitation) wherein they stack laterally at a distance of approximately 4.1 Å
[50]. This registry condition implies that, upon deposition, alkylated compounds search for the
most favourable adsorption site on the HOPG surface such that the molecule–substrate and
molecule–molecule van der Waals interactions are maximized.
Comparative studies describing the adsorption of a single building block on two different
substrates are relatively scarce [51]. Nevertheless, one readily expects that the substrate lattice
and thus the registry effects will be different for different substrates, which implies that the
strength of molecule–substrate interactions will also be different. This influences the mobility of
adsorbing species, which subsequently affects their ability to act as nucleation sites for growth of
the network. Apart from simple, single-component systems, substrate effects also play a pivotal
role in the formation of complex multi-component supramolecular networks, as illustrated by a
comparative study of a three-component network carried out on Au(111) and HOPG [40].
Alkoxylated dehydrobenzo[12]annulene (DBA) derivatives (figure 1a) form honeycomb
porous networks which are stabilized by van der Waals interactions between interdigitated pairs
of alkyl chains. The rim of each hexagonal nanowell consists of a pair of alkyl chains from one
DBA molecule, interdigitated with a pair from an adjacent molecule. When adsorbed on a surface,
this interdigitation becomes chiral with two distinct interdigitation motifs, labelled arbitrarily (−)
and (+) (figure 1b). The combination of interdigitation motifs within an individual nanowell can
produce either chiral or achiral nanowells. Chiral nanowells have a combination of six identical
interdigitation motifs. A chiral nanowell with all (−)-type interdigitation motifs leads to the
formation of a so-called counterclockwise (CCW) nanowell, whereas the one with all (+)-type
interdigitation motifs forms the clockwise (CW) nanowell (figure 1b) [52]. In the absence of any
chiral influence, DBA on HOPG forms networks with equal amounts of domains containing CCW
and CW nanowells, and the chirality of the nanowells is domain specific [15]. Achiral pores, on the
other hand, have a combination of three (−)- and three (+)-type interdigitation motifs arranged
in an alternating pattern (figure 1b).
Varying the alkyl chain length of DBA allows the pore size to be tuned to trap specific
guest molecules or clusters to form multi-component systems. The nanowells formed by DBA
with dodecyloxy chains can trap a heterocluster formed by one coronene (COR) and six
isophthalic acid (ISA) molecules. The self-assembly of this multi-component system at the liquid–
solid interface between Au(111) or HOPG and organic solvents results in different types of
supramolecular networks. On Au(111) substrates, multi-component networks display an ordered
superlattice arrangement of chiral and achiral pores (figure 1c,e). In comparison, similar networks
on HOPG display only chiral pores (figure 1d,f) [15]. The unique superlattice structure observed
on Au(111) could be related to a lower energetic preference for chiral pores than on HOPG and
increased diffusion barriers for guest molecules. The increased diffusion barriers for guests allow
them to act as nucleation sites for the formation of achiral pores. Following the initial nucleation of
an achiral pore, restrictions imposed by the accommodation of guests within the porous network
mean that subsequent growth naturally leads to the formation of the superlattice structure [40].
The medium from which the molecules adsorb on the surface is another fundamental
parameter that can significantly influence the molecular organization on substrates. It strongly
determines the deposition conditions and the related thermodynamic or kinetic parameters
of the self-assembly process. Under UHV conditions, molecules are generally evaporated or
alternatively a solution of them is sprayed onto the substrate by using a spray valve. A key
advantage of working under UHV conditions is that one can obtain superior control over the
surface coverage as well as temperature. Moreover, by using low and high temperatures, one
can address kinetically trapped and thermodynamically equilibrated structures, respectively.

5
......................................................
(a) (b)
R
R
R
R=OCnH2n+1
R
HO
R COR CCW
(+)-type
+
+
+
–
–
–
achiral
(mixed)(–)-type
CW
O OH
O
ISA
3nm
2nm
DBA
R
(c) (d)
(e) ( f )
Figure 1. Substrate dependence of complex multi-component supramolecular networks. (a) Molecular structures of DBA,
coronene and isophthalic acid. (b) Molecular models depicting the (+)- and (−)-type interdigitation patterns leading to the
formation of chiral CCW and CW nanowells, respectively. A combination of three (+)-type and three (−)-type interdigitation
patterns yields an achiral pore. (c) Three-component network formed at the 1-octanoic acid/Au(111) interface along with the
molecular model (e). (d) Three-component network formed at the 1-octanoic acid/HOPG interface. Only chiral nanowells are
formed. (f) Molecular model for the network formed on HOPG. (c,e) and (d) have been reproduced from references [40] and
[15], respectively, with permission from the American Chemical Society. (Online version in colour.)
The presence of a vacuum above the monolayers does not limit the temperatures accessible for
inducing (or reducing) dynamics when compared with monolayers formed at the liquid–solid
interface where the presence of organic solvents restricts the annealing conditions. However,
owing to its simplicity, the liquid–solid interface has gained immense popularity to assemble
molecules in two dimensions.
The solvents used in STM studies at the liquid–solid interface are often chosen for practical
reasons: they should dissolve the molecules of interest but not compete with them for surface
adsorption, they should be chemically inert and they should have a low vapour pressure.
Despite numerous investigations, the role of solvents in molecular self-assembly at the liquid–
solid interface is less clearly understood. In the most ‘active’ mode of participation, the solvent

6
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q q
q
q
g g
g
g
4nm 4nm
4nm
4nm
a
a
a
a
b
b
b
b
(a) (b) (e)
(c) (d)
( f )
Figure 2. Solvent-induced homochirality in mono- and multi-component networks obtained at the interface between
enantiopure 2-octanols and HOPG. (a) CCW honeycomb motif formed preferentially at the (S)-2-octanol/HOPG interface. (b)
CW honeycomb motif formed preferentially at the (R)-2-octanol/HOPG interface. Molecular models shown in (c,d) reproduce
the molecular packing in (a,b), respectively. (e,f) Homochiral three-component supramolecular networks consisting of COR–
ISA6heteroclusterstrappedbyvoidsofDBAhostnetworksformedfrom(S)-2-octanoland(R)-2-octanol,respectively.Adapted
from reference [23] with permission from the American Chemical Society. (Online version in colour.)
molecules undergo co-adsorption with the adsorbate molecules to form a multi-component
monolayer. Solvent-induced polymorphism, the effect of co-adsorption as well as the solvent
effects on electronic structures have been summarized recently [27].
In addition to their role as dispersing media, chiral enantiopure solvents can influence the
handedness of the molecular networks formed at the liquid–solid interface [23,29]. The self-
assembly of achiral DBA derivatives at the interface between enantiopure 2-octanol and HOPG
resulted in the formation of homochiral monolayers in which the handedness of the porous
supramolecular networks was determined by the handedness of the solvent. Self-assembly of
DBA derivatives at the (S)-2-octanol/HOPG interface led to preferential formation of the (+)-
type interdigitation pattern and thus the CCW honeycomb motif (figure 2a,c). On the other hand,
(R)-2-octanol induced a clear bias towards preferential formation of the (−)-type interdigitation
pattern and hence the CW honeycomb motif (figure 2b,d). The solvent-induced homochirality in
these monolayers could also be discerned from the preferred orientations of the DBA networks
with respect to the normal to the HOPG symmetry axis [23].
The assembly process consisted of recognition between a particular handed solvent molecule
and the specific type of interdigitation pattern during the early stages of nucleation. A notable
aspect of this solvent-mediated chirality transfer experiment was that the homochiral porous
networks preserved their handedness even when the voids were occupied by guest clusters
of COR and ISA (figure 2e,f). Thus, it is possible to store chiral information in the structure
of the solvent molecules and then this information can be transferred to the multi-component
supramolecular networks formed at the interface between such chiral solvents and an achiral
substrate [23].
4. Role of concentration
When studying two-dimensional assembly at the liquid–solid interface, the number of molecules
adsorbed at the interface as well as those present in the supernatant solution is extremely
crucial and can be controlled by manipulating the solute concentration. Careful control over
concentration can aid in selecting a specific structure, especially when two or more polymorphs
are possible that differ in packing density or adsorption energy [30–35]. One of the first
examples of concentration-dependent self-assembly was discovered in the case of alkoxylated
DBA derivatives [30].

7
......................................................
(c) (d)100
dilution
10nm10nm 5nm30nm
OC12
OC14
OC16
OC18
80
60
40
q(%)
0 2
concentration ×10–4
moll–1
4 6 8
20
0
(a) (b)
Figure 3. Concentration-controlled polymorphism in the monolayers of DBA–OC16 at the TCB/HOPG interface. (a,b) The high-
density linear and low-density honeycomb networks obtained using high and low concentrations of DBA–OC16, respectively.
The insets show magnified regions of STM images. (c) Schematic illustration of the linear to porous transition. (d) Dependence
ofsurfacecoverageofthehoneycombpattern(θ)ontheDBAconcentrationfordifferentDBAderivatives.(a,b,d)Adaptedfrom
reference [30] with permission from Wiley-VCH. (Online version in colour.)
When the solution concentration is relatively high, DBA derivatives form a high-density
linear packing, whereas at relatively lower concentrations, low-density nanoporous networks are
obtained. Both polymorphs coexist at intermediate concentrations. The relative coverage of each
polymorph thus could be controlled by meticulous choice of solution concentration. The STM
images displayed in ﬁgure 3 clearly illustrate the concentration-dependent surface coverage of the
linear and porous honeycomb networks for a DBA–OC16 derivative. A systematic examination
of the concentration-dependent self-assembly of DBA derivatives with different alkoxy chain
lengths, however, revealed that the concentration range in which this transformation is observed
depends on the alkyl chain length. The surface coverage of the honeycomb network follows a
linear relation with concentration for DBA derivatives with smaller alkoxy chains, whereas for
DBA derivatives with longer alkoxy chains this relation is exponential (ﬁgure 3d) [30].
To further understand the mechanism of concentration-controlled structure selection of DBA
derivatives at the liquid–solid interface, a thermodynamic model [30] was proposed which
describes how the relative surface coverage correlates with concentration and temperature.
Assuming that there exists an equilibrium between the molecules adsorbed in two polymorphs
and the molecules present in solution, at full surface coverage, a measure of the relative coverage
of the two polymorphs can be expressed as
Yh
Y
(l/h)
l
= e((μ0,solution−μ0,h)−(l/h)(μ0,solution−μ0,l)/kBT)
c(1−l/h)
, (4.1)

8
......................................................
(a)
(b)
H3
C O
O
NH2
17
(c)
II
III IV
V
(d)
6.3nm
2.6nm
5.3nm
(e)
Figure 4. Concentration-controlled polymorphism in the monolayers of a C18 amide at the 1-phenyloctane/HOPG interface.
(a) Molecular structure of C18 amide. (b,c) Close-packed structures obtained from relatively concentrated solutions.
(d,e) Low-density nanoporous networks formed at relatively lower concentrations. Molecular models reproducing the packing
of molecules in respective monolayers are also given near the STM images. Adapted from reference [34] with permission from
the American Chemical Society. (Online version in colour.)
where Yh and Yl are the surface coverages of the honeycomb porous and linear networks,
respectively, and h and l are the numbers of molecules per unit area in the respective pattern.
μ0,solution, μ0,h and μ0,l are the chemical potentials of the molecules in solution, in the honeycomb
and in the linear packing, respectively. This expression reproduces the experimental trend and
describes how lowering the concentration c results in an increase in the ratio of the surface
coverage of the honeycomb versus linear network. The two variables in equation (4.1), namely
concentration c and temperature T, can thus be used to tune the relative surface coverage of
the different polymorphs. The nature of the solvent is reflected in the chemical potential term
μ0,solution, which is related to the solvation enthalpy, whereas μ0,h, and μ0,l are characteristic for
different adsorbates and their adsorption geometries on the surface and are related to adsorption
enthalpy. As derivation of equation (4.1) is general and independent of the choice of adsorbate,
solvent or substrate, it should in principle hold for all self-assembling systems in which one
component can assemble into two different polymorphs [30].
The concentration-in-control principle has since been confirmed by various other studies [31–35].
The concentration effects, however, are not limited to high-symmetry molecules. Ahn & Matzger
[34] demonstrated that a low-symmetry amide amphiphile can overcome geometric barriers
to build highly symmetric monolayers using the concentration control strategy. For an amide
with an octadecyloxy chain (figure 4a) adsorbed at the 1-phenyloctane/HOPG interface, they
could observe as many as four different polymorphs with varying stabilities and densities. At
relatively high concentrations (1.0 × 10−4 M), phase II is the major polymorph (figure 4b) along
with phase III which appears as a minor structure (figure 4c). Upon reducing the concentration,
within a concentration range of 3.3 × 10−5 M to 5.0 × 10−4 M, two different types of nanoporous
networks were visualized—namely, a rhombic nanoporous network (figure 4d) and a honeycomb
porous network (figure 4e). The rhombic network is the preferred polymorph formed from dilute
solutions. As this bonding pattern is kinetically not easily accessible, polymorph IV is formed
initially, which transforms into thermodynamically favoured polymorph V.
The respective stabilities of these polymorphs at given concentrations were confirmed by
changing the concentration in situ by addition of 1-phenyloctane. For example, when the
concentration of solution was decreased by adding solvent, a gradual phase transformation
from phase II to phase V via phase IV was observed. As at no concentration was phase IV

9
......................................................
(a) 55°C
25°C 25°C 25°C
55°C 55°C10nm
10nm 10nm 10nm
10nm 10nm
(c)
(b) (d)
(e) (g)
( f )
COOH
COOHBTBHOOC
Figure 5. (a) Molecular structure of BTB. (b–g) Temperature-induced reversible phase transitions in the monolayers of BTB at
the 1-nonanoic acid/HOPG interface. The respective temperatures are stated in the lower or upper left corner of each image.
Adapted from reference [45] with permission from the American Chemical Society. (Online version in colour.)
observed as a stable polymorph, it was concluded that it is only kinetically accessible and
not thermodynamically stable. In addition to its fundamental interest, the concentration
dependence of self-assembly provides an elegant way of fabricating several energetically viable
supramolecular aggregation patterns by simply manipulating the solute concentration [34].
5. Role of temperature and thermal history
It is apparent from equation (4.1) that, besides concentration, temperature is an essential
parameter governing the self-assembly process as it affects both the thermodynamics as well as
the kinetics of the system. Despite this fact, among all the important parameters critical to the
self-assembly process, the temperature effect on the self-assembly at the liquid–solid interface is
the least studied [42–45,53]. Although variable temperature experiments under UHV conditions
are done routinely, very often samples are conditioned at elevated temperature, whereas the STM
measurements are still carried out at room temperature or cryogenic temperatures.
In a recent study, Lackinger and co-workers [45] addressed the temperature dependence
of molecular self-assembly at the liquid–solid interface by in situ STM visualization of
temperature-induced phase transitions in the monolayers of 1,3,5-tris(4-carboxyphenyl)benzene
(BTB) (figure 5a). Self-assembly of BTB at the 1-octanoic acid/HOPG interface, at room
temperature, leads to emergence of two different polymorphs; namely, a high-density row
structure (figure 5c) and a low-density porous structure (figure 5b). However, the high- and the
low-density polymorphs could be obtained exclusively when the self-assembly is carried out from
1-heptanoic and 1-nonanoic acid, respectively. Heating the BTB/1-octanoic acid/HOPG system
(where both polymorphs coexist) above 43◦C leads to a phase transition wherein the entire surface
gets covered with row structure. Similarly, the low-density porous polymorph formed at the
1-nonanoic acid/HOPG interface transforms into the high-density row structure above 55◦C.
These structural transitions could be induced reversibly by variation of temperature above and
below the transition temperatures mentioned above [45].
Both of the polymorphs are assumed to be thermodynamically stable under given
experimental conditions, and the reversibility of the transition process further confirms that the
porous network obtained at relatively lower temperatures is not merely a kinetically trapped
structure. Adsorption of molecules at the liquid–solid interface represents a trade-off between
solvation and adsorption enthalpy. While a favourable adsorption enthalpy helps to minimize
the Gibbs free energy, the accompanying loss of entropy upon adsorption acts against it. For
this reason, the enthalpic and entropic contributions to the Gibbs free energy are important. A

10
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1.0
OR
OR
OR
RO
RO(a) OR
TSB
N=1
N=2
N=5
N=10
N=20
N=100
data
0.8
0.6
0.4
0.2
0
10–6
fractionofthesurfacecovered
bythehoneycombstructure(Yporous)
10–5
concentration (moll–1)
10–4 10–3
(b)
(c)
(d)
Figure 6. Influence of growth history on monolayers. (a) Molecular structure of TSB. (b) Monolayer of TSB obtained upon
deposition of solution on HOPG held at lower temperature and then annealing at 60◦
C for 1 h. (c) Monolayer structure upon
depositionontoHOPGheldat60◦
Cfollowedbyannealingat60◦
Cfor1 h.(d)Aplotshowingthefractionofthesurfacecovered
bytheporousnetworkasafunctionofconcentrationalongwithcalculatedcurves.Adaptedfromreference[46]withpermission
from the American Institute of Physics. (Online version in colour.)
reduction in the degrees of freedom upon adsorption implies a reduction in the entropy, which
increases the Gibbs free energy of the system. As a consequence, spontaneous self-assembly
of molecular components necessitates that the loss of entropy at a given temperature must
be compensated by gain in enthalpy upon adsorption. The authors used molecular mechanics
calculations to compute binding enthalpies, whereas the changes in the entropy were estimated
using a method proposed by Whitesides and co-workers [54]. The thermodynamic model
developed using these estimates could be fully understood only when solvent coadsorption in
the voids of the nanoporous networks was taken into account. Using this approach, they could
quantitatively estimate the changes in Gibbs free energy for the two phases of BTB and also
reproduced the experimental trend for phase transitions [45].
Charra and co-workers [46] demonstrated that not only the annealing temperatures but also
the growth history of the sample is critical in the selection of a particular polymorph in an
equilibrating system. Similar to the DBA derivatives discussed in previous sections, dodecyloxy
substituted 1,3,5-tristyrylbenzene (TSB; figure 6a) self-assembles into a high-density linear
(figure 6b) and a low-density honeycomb porous (figure 6c) polymorph at the 1-phenyloctane/
HOPG interface. STM images recorded immediately after application of a droplet of TSB solution
onto the HOPG substrate held at 21◦C revealed only disordered aggregates. This system was then

11
......................................................
allowed to equilibrate for 1 h, during which the substrate was held at 60◦C. STM visualization of
such a sample revealed the formation of large domains of densely packed polymorph. In the
second experiment, the TSB droplet was applied onto HOPG held at 60◦C and the temperature
was held constant for 1 h. This led to the formation of large domains of porous molecular
networks. These experiments demonstrate that, for a given final temperature and concentration,
the characteristics of the adsorbed monolayer strongly depend on its growth history, that is, on
the detailed sequence of temperatures applied during and after the solution droplet deposition.
The authors assimilated these observations by considering different nucleation and growth rates
for the two polymorphs and argued that, even at relatively high temperatures, a kinetic blockade
prevents the transition of the thermodynamically less stable porous structure to the more stable
high-density linear structure [46].
Temperature evolution of the percentage surface coverage for the honeycomb network of
different TSB derivatives revealed that sharp phase transitions appear at precise concentrations.
This observation is in contrast to the one made in the case of DBA derivatives, wherein the
phase transitions were more gradual. The authors addressed this discrepancy by considering the
equilibrium between molecules in solution and entire domains of the two polymorphs instead of
independent molecules adsorbed in dense and porous domains. Thus, the thermodynamic model
takes the form
Yh
Y
(l/h)
l
1/N
= e((μ0,solution−(1/N)μ0,h)−(l/h)(μ0,solution−(1/N)μ0,l)/kBT)
c(1−l/h)
. (5.1)
The factor 1/N in equation (5.1) is the only mathematical change compared with the expression
given in equation (4.1). It is a dimensionless parameter in the redefined chemical potential term
for two-dimensional aggregates of aggregation number N and accounts for molecular interactions
responsible for domain formation instead of disordered aggregates. For N = 1, equation (5.1)
reduces to equation (4.1). For larger values of N (for example, N = 100), this model could
reproduce the sharp phase transitions observed by the authors (figure 6d) [46].
6. Dynamics and phase transitions in two-dimensional monolayers
It is clear from the discussion presented in previous sections that, apart from thermodynamics,
kinetics too plays an important role in the self-assembly process. The dynamics during early
nucleation events and also after the surface is covered with molecules determines whether the
monolayer represents a kinetically trapped metastable or thermodynamically stable equilibrated
state. Apart from the spontaneous dynamics inherent to each system, the movement of molecules
can be induced by external stimuli such as light [55–57], interactions with the STM tip
[58], changes in electrical potential [59], molecular additives [60–62] and, as discussed in the
previous section, changes in temperature [42–45,53]. These dynamic phenomena assume special
importance in the context of phase transitions in two-dimensional molecular systems.
Ernst and co-workers [63] reported temperature-controlled reversible phase transitions in
the monolayers of bowl-shaped corannulene molecules at the UHV/Cu(111) interface. At room
temperature, a regular array of molecules is formed (figure 7e). Reduction in the substrate
temperature leads to two different phase transitions. A denser lattice is formed at 225 K (figure 7f),
and it converts to another structure (figure 7g) upon further cooling of the substrate to around
69 K. These transitions are reversible, and it was possible to revert back to the room temperature
phase via the intermediate phase upon heating the substrate. The subsequent phase transitions
caused a 14.3% increase in the lattice density upon cooling the substrate.
The asymmetrical appearance of the molecules indicates that they are substantially tilted on
the Cu(111) surface. Furthermore, from the comparison of the lattice parameters, the authors
confirm that the intermediate phase is formed owing to the compression of molecules along one
lattice direction. Cooling of the room temperature phase leads to wiggling motions of molecules
in every alternate row (identified from different STM contrasts) and further leads to zipper-like

12
......................................................
(a) (b)
cool
heat
(e) ( f )
4 0
0 4
4 0
3 7
4 2
0 7
(g)
(c) (d)
Figure 7. Reversible phase transitions in the monolayers of corannulene on Cu(111). (a) Ball and stick model of corannulene.
(b–d) Correlation of the STM contrast with molecular structure, revealing a tilted adsorption geometry of molecules on the
Cu(111)surface.(e)Roomtemperaturephase.(f)Intermediatetemperaturephaseformedat225 K.(g)Low-temperaturephase
obtaineduponfurthercoolingto69 K.Adaptedfromreference[63]withpermissionfromWiley-VCH.(Onlineversionincolour.)
displacement of several adjacent molecules. The migration proceeds via the fcc to hcp threefold
hollow sites of the copper lattice. The second transition does not involve any change in the
lattice density but a mere rearrangement to adjust to the most favourable fcc threefold hollow
site. The compression of molecular lattice was explained by considering the breathing mode
vibrations of the molecules at room temperature, which require larger space on the substrate.
Cooling of the system leads to suppression of these vibrational modes and thus decreases the
spatial requirements of the molecules, enabling closer packing [63].
Molecular dynamics and thus phase transitions can also be induced by using light irradiation
if the supramolecular network contains light responsive functional units. Azobenzene-based
organic building blocks have often been used to extract reversible photoresponse [56,57] from
molecular nanostructures. Gong and co-workers [55] exploited the photosensitive azobenzene
groups to realize reversible phase transitions in a complex three-component system. The building
block used consisted of a 4NN-macrocycle (figure 8b) containing four azobenzene units. This
molecule could be immobilized by using a molecular template formed by TCDB molecules
(figure 8a). The 4NN-macrocycle adsorbs with all its azobenzene units in the all-trans (t,t,t,t)
conformation. Addition of COR to this two-component network does not lead to significant
changes in the dimensions of the lattice parameters. COR molecules are not immobilized into
the cavities of the 4NN-macrocycle but rather sit atop the monolayer (figure 8e) [55].

13
......................................................
COOH
(a)
0
0
5 10
10
visible light UV visible light UV
coronenecoronene
b
b
a
a
20
0 10 20
0nm
nm
5
10
20
10
0
nm
20
10
0
(c) (d)
(e)
(g) (h)
( f )
(b)
8
N
N
N
4NN-macrocycleN
NN
N
N
OO
O
8
8HOOC
COOH
TCDB
a
a
Figure 8. Photoswitchable ternary supramolecular network formed at the 1-heptanoic acid/HOPG interface. (a,b) Molecular
structures of TCDB and the 4NN-macrocycle. (c,d) Two-component network consisting of TCDB and the 4NN-macrocycle. (e,f)
The three-component system prior to UV irradiation. (g,h) The three-component system after UV irradiation. The immobilized
coronene molecules could be visualized clearly. Adapted from reference [55] with permission from the American Chemical
Society. (Online version in colour.)
Upon UV irradiation, a new supramolecular arrangement is observed in which the voids of the
host network are occupied by immobilized COR molecules. The shape of the macrocycle changes
from parallelogram to ellipsoidal after irradiation, and it is attributed to the photoinduced trans
to cis isomerization of the two azobenzene units which transform the macrocycle from the (t,t,t,t)
to the (t,c,t,c) conformation. This transformation increases the effective area of the voids and thus
COR molecules are immobilized in the voids to form a well-ordered array of host–guest type
network. The reverse process of the transformation of the cis conformation back to the more
stable all-trans conformation is induced by irradiation with visible light, in which case the COR
molecules are expelled from the pores owing to shrinkage of the porous voids. Such reversible
phase transformations are central to the development of molecular-scale switches [55].
7. Thermodynamics of reactions and catalysis in two-dimensional monolayers
Temperature control of self-assembly provides valuable information concerning diffusion and
reaction rates, activation energies and thermodynamic parameters such as the entropy and
enthalpy of various processes including surface-supported reactions and catalysis. Although
relatively nascent, an increasing number of researchers are addressing the thermodynamic
and kinetic aspects of these processes. Such investigations are immensely important from a
commercial point of view owing to their relevance to heterogeneous catalysis.

14
......................................................
0.30
5nm
0.20
0.18
0.16
0.14
0.12
0.10
0.08
0.06
0.04
0.02
1 2 3
distance (nm)
apparentheight(nm)
4 5 6 7
0
0
(b)
(a)
(d)
(c)
Q/(1–Q)
0.25
0.20
0.15
0.10
0.05
0 200
partial pressure of O2
(Torr)
400 600
Figure 9. Oxygen binding of molecular oxygen to CoOEP at the liquid–solid interface. (a) Model for the CoOEP. (b) Plot of the
relative surface coverage of oxygenated species against partial pressure of O2. (c) STM image of CoOEP at the 1-phenyloctane–
HOPG interface. White circles highlight the molecules with bound oxygen, whereas white squares show vacancies in the
monolayer. (d) A schematic illustrating the oxygen-binding process on the HOPG surface. Adapted from reference [64] with
permission from the American Chemical Society. (Online version in colour.)
In a recent study, Hipps and co-workers [64] studied the thermodynamics of the reversible
binding of oxygen to cobalt (II) octaethylporphyrin (CoOEP; figure 9a) adsorbed at the
1-phenyloctane/HOPG interface. The monolayer of CoOEP adsorbed at 25◦C in equilibrium with
pure O2 shows varying STM contrast (figure 9c). Some molecules appear brighter than others and
the authors interpreted the darker features as molecules with axially bound O2. An increase in
the partial pressure of O2 led to an increase in the number of dark molecules in the monolayer
(figure 9b). The oxygen-binding process follows the Langmuir isotherm in which the relative
surface coverage of dark molecules is proportional to the partial pressure of O2. Using this plot,
the authors calculated the equilibrium constant for O2 adsorption, which was further used to
calculate the free energy change for the binding process. By carrying out STM measurements at
different temperatures and at 100% O2 saturation, the authors obtained a plot of the free energy
change versus the temperature, the slope of which corresponds to the entropy change of the
process relative to the standard state. From this value of entropy, it was possible to calculate the
enthalpy changes associated with the process [64].
Thus, all the thermodynamic parameters associated with the O2-binding process could be
obtained from STM measurements. The enthalpy and entropy changes were found to be larger
than those reported for solution-phase experiments for the same process. The authors point out
that room temperature binding of O2 to CoOEP is generally impossible under solution conditions
and it is made feasible owing to the adsorption of molecules on the HOPG surface. The stability
of the bound oxygen was attributed to the charge donation from the graphite surface, which

15
......................................................
0.7
(a)
(e)
(c)
(d)
(b)
NH2 CHO
–H2
O
one-dimensional macromolecular adlayer
extended two-dimensional network
reaction
equilibrium
reaction
equilibrium
adsorption
equilibrium
adsorption
equilibrium
surface diffusion
surface diffusion
surface-selective
polycondensation
surface-selective
polycondensation
N=C
HH2
Oabs.@335nm
monomeric
dispersion
reaction
condition
irreversible
sedimentation
0.6
0.5
0.4
0.3
0.2
0.1
1 2
R R
N
N
R=NN
RR
N
N
H
H
OHC
OHC
OHC
OHC
CHO
S
TPA
TCA
IPA
BCA
S S
CHO
CHO
CHO
NH2
NH2
NH2
H2
N
H2
N
3 4
ASB
ADA
TAPP
pH
5 6 7
0
amineunits
aldehydeunits
Figure 10. Thermodynamically controlled polycondensation reaction at the liquid–solid interface. (a) General reaction
scheme. (b) pH-dependent absorbance of the solution containing a mixture of 4,4 -diaminostilbene dihydrochloride (ASB)
and terephthaldicarboxaldehyde (TPA). (c,d) Schematic of the equilibrium processes leading to formation of extended one-
dimensional and two-dimensional covalent networks, respectively. (e) Molecular building blocks used for the surface selective
polycondensation reaction. Adapted from reference [68] with permission from the American Chemical Society. (Online version
in colour.)
essentially acts as a ﬁfth ligand [64]. The ability of a surface to act as an additional ligand for
porphyrins was reported earlier by Elemans and co-workers [65] for alkylated Mn-porphyrin
monolayers adsorbed at the tetradecane/Au(111) surface.
Recent years have witnessed a surge in reports describing surface-supported synthesis and
STM of two-dimensional covalent networks [66–70]. Selective intermolecular interactions have
been widely exploited to couple non-covalently assembled molecular components in a more
‘permanent’ covalent fashion. Initial attempts to synthesize such two-dimensional covalent
organic frameworks (COFs) were limited to the UHV systems. In general, the UHV experiments
used kinetically controlled, thermally activated reactions conducted at very low surface coverages
in order to control the supply of molecular building blocks to prevent undesired side reactions.
Kunitake and co-workers [68] provided a breakthrough in the much sought after ambient
solution/solid interface synthesis of two-dimensional COFs recently by covalent linking of a
series of aromatic aldehydes and amines. An advantage of such equilibrium-controlled covalent
coupling is that it eliminates the necessity for severe conditions and sophisticated equipment.
Figure 10 shows the general concept of the covalent coupling methodology developed by
the authors. It consists of an equilibrium polycondensation reaction between aromatic primary
amines and aldehydes to form two-dimensional COFs. This reaction is reversible when carried
out under mild aqueous solution conditions.
By exploring the thermodynamic control of the reaction conditions by carefully varying the
pH of the system, they could successfully fabricate various π-conjugated polymers on an iodine-
modiﬁed Au(111) substrate. The visualization of the two-dimensional COFs was carried out using

16
......................................................
electrochemical STM. The reversibility of the reaction under given conditions coupled with the
reversibility of the adsorption and non-covalent network formation at the liquid–solid interface
led to formation of extended covalent networks under solution conditions. As the process is not
limited to two-dimensional structures, it can be readily applied to arbitrary three-dimensional
COFs as well.
8. Summary and outlook
A steadily growing number of researchers from diverse disciplines are exploring the
opportunities brought forward by the research on molecular self-assembly. A common goal
is the fabrication of supramolecular nanostructures in a controlled and reproducible manner.
A prerequisite for achieving this goal is the precise understanding of the thermodynamic
and kinetic parameters that govern the self-assembled network formation. Although many of
the supramolecular interactions that exist in the three dimensions can be translated to build
nanostructures in two dimensions, care must be taken when extending the concepts in three
dimensions to two dimensions and vice versa because the presence of a substrate and solvent
complicate the two-dimensional self-assembly process. For example, concentration-dependent
polymorphism in crystal structures is alien to three-dimensional crystallizations, whereas it is
routinely observed in the case of two-dimensional self-assembled monolayers.
A number of thermodynamic and kinetic models have been proposed to address phenomena
that are unique to nanostructures formed at liquid–solid interfaces. Concentration- and
temperature-dependent changes in two-dimensional nanostructures have been assimilated
using such thermodynamic models. Despite the understanding developed so far, a number
of parameters that are crucial to the self-assembly process at these interfaces lack a thorough
theoretical and sometimes even experimental description. For example, the thermodynamic
models that accommodate solvent-related parameters such as solvation enthalpy (related to the
thermodynamics of the system) and viscosity (related to the diffusion rates and hence the kinetics
of the system) have not been developed yet. An exciting development is the real-time and real-
space exploration of chemical reactions and catalysis which can lead to unique covalently linked
two-dimensional nanostructures. An increasing number of studies are addressing these issues,
which will help in the development of more rational approaches for the fabrication of molecular
nanostructures.
Acknowledgements. In particular, we thank the group of Prof. Tobe from Osaka University for very fruitful
collaboration. In addition, Prof. Sheng-bin Lei from the Harbin Institute of Technology is acknowledged for
his contribution.
Funding statement. This work is supported by KU Leuven through GOA 2006/2, Funding for Scientiﬁc
Research—Flanders (F.W.O.) and the Belgian Federal Science Policy Ofﬁce through IAP 7/05.
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